Research workbench
Structure of H2-treated anaerobically purified D. fructosovorans nife- hydrogenase
Analyse Structure of H2-treated anaerobically purified D. fructosovorans nife… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UEW
- Type
- protein
- Length
- 2,417 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic [nife] hydrogenase small subunit; Periplasmic [nife] hydrogenase large subunit
- EC
- 1.12.2.1
- UniProt
- P18187, P18188
- Ligands
- SF4, F3S, FCO, NI, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Periplasmic [nife] hydrogenase small subunit (EC 1.12.2.1) | protein | 262 | 37% helix, 17% strand | P18187 |
| C | Periplasmic [nife] hydrogenase small subunit (EC 1.12.2.1) | protein | 260 | 37% helix, 17% strand | P18187 |
| Q, S | Periplasmic [nife] hydrogenase large subunit (EC 1.12.2.1) | protein | 544 | 48% helix, 16% strand | P18188 |
| R | Periplasmic [nife] hydrogenase large subunit (EC 1.12.2.1) | protein | 545 | 49% helix, 16% strand | P18188 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, Q, B, R, C, S
- F3S · FE3-S4 cluster · ligand · 3 copies · chains A, Q, B, R, C, S
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 3 copies · chains Q, R, S
- NI · Nickel (II) ion · metal · 3 copies · chains Q, R, S
- MG · Magnesium ion · metal · 3 copies · chains Q, R, S
- GOL · Glycerol · additive · 14 copies · chains A, Q, C, B, R, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.82 | 0.97 | 53 | empty |
| 2 | 1084 | 0.80 | 0.81 | 75 | empty |
| 3 | 801 | 0.80 | 0.83 | 95 | empty |
| 4 | 103 | 0.78 | 0.97 | 34 | empty |
| 5 | 69 | 0.72 | 0.96 | 25 | empty |
Interfaces
8 interfaces between chains.
- B–R · 3604 Ų buried · 58 hydrogen bonds · protein-protein
- A–Q · 3582 Ų buried · 60 hydrogen bonds · protein-protein
- C–S · 3568 Ų buried · 53 hydrogen bonds · protein-protein
- C–R · 521 Ų buried · 6 hydrogen bonds · protein-protein
- C–Q · 455 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 modified (disulfide, oxidation).
Compared structures
- 4UEW · Structure of H2-treated anaerobically purified D. fructosovorans NiFe- hydrogenase · the same entry in another collection · chain S against S, TM-score 1.00
- P18188 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase large subunit… · a predicted model of the same protein · chain Q against A, TM-score 1.00
- P18187 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase small subunit… · a predicted model of the same protein · chain C against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P18187
- Every structure of UniProt P18188
- Elsewhere: RCSB PDB 4UEW · PDBe 4UEW · UniProt P18187 · UniProt P18188
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